Honestly, there's really nothing we can to to help troubleshoot this third-party issue. That tracking code is just a javascript that runs in the buyer's own browser when it loads the page. We send it to to their browser exactly as you specify it in your Thank-you Page customization fields. If you have specified any [%template_variables%] in your Thank-you Email customization fields, we simply replace those with their respective values before sending your code to the buyer's browser.
To view the actual thank-you page generated for each transaction, you can go into your Seller Admin > View/Download Transaction Log, then find the transaction and click on its Transaction ID to bring up its thank-you page. Then you can View Source for that page to see how your tracking code is actually being sent to the buyer's browser and troubleshoot from there.